Listed as Endangered as the species is suspected to have undergone a population decline of ≥50% over a period of 30-36 years (three generations), due primarily to continuing decline in area, extent and quality of habitat, and exploitation through unsustainable levels of hunting. These causes have not ceased, and will to a large extent not be easily reversible. A population reduction of ≥50% over the next 1-2 generations (10-24 years) is also projected due to the same causes.

Although mainly reported from eastern, northern and central-western parts of the island, this species evidently occurs in fragmented pockets (though in very low population densities) across almost the whole of coastal Madagascar. Recent confirmed sightings document its presence in the eastern forests from Ampanefana in the north to Andohahela National Park in the south, and in the western and northern forests from Montagne d' Ambre in the north to at least Tsingy de Bemaraha National Park in the south. There are also two introduced island populations off the coast of northeastern Madagascar, one on Nosy Mangabe in the Bay of Antongil, and the other on Ile Roger (a.k.a. "Aye-aye Island") at the edge of the town of Mananara-Nord. Whether the species formerly existed on the island of Nosy Mangabe remains uncertain, but subsequent expeditions have confirmed its continued survival there since its mid-1960s introduction. It occurs from sea-level to 1,875 m.

Based only on signs and infrequent sightings, the species is known to occur in many different habitat types and regions. Population numbers are certainly in decline however due to habitat loss and hunting. There is little understanding of population size and dynamics. Daubentonia madagascariensis is suspected to have the lowest genetic diversity of all the lemur taxa (S. Johnson pers. comm).

Sightings of D. madagascariensis are rare; its presence is often assumed from tree hole marks. Abundance is also hard to estimate, as one individual is capable of making numerous marks. The nocturnal Aye-aye is quite adaptable and is known from a variety of habitats including primary rain forest, deciduous forest, secondary growth, dry scrub forest, and mangrove swamps. The species has also been noted to occur in cultivated areas; however these are marginal, unsuitable, habitats. The southern spiny desert appears to be the only habitat in which the species does not occur. Its presence in many areas appears to be determined largely by its primary food resource, the seeds of ramy (Canarium spp.) although there are also other dietary staples (Mittermeier et al. 2008, and references therein). During the day, D. madagascariensis sleeps in nests, tree forks or vine tangles. Nests may be occupied for a few days at a time and several individuals may use the same nest at different times.Daubentonia madagascariensis has vast home ranges which exceed 600 ha; interestingly, individuals appear to spend more time moving along the ground than any other lemur except Lemur catta (Sterling 1993). Recent evidence suggests that Aye-ayes are not strictly solitary, but also forage in tandem and may exhibit differing relationships between animals of the same sex (Sterling and Richard 1995). There appears to be no restricted mating season and a single young is born. Females begin breeding at three or four years, and indications are that females give birth every two to three years (Petter and Peyrieras 1970).

These animals are killed in some areas as a harbinger of evil/symbol of bad luck and as a crop-pest (e.g., coconuts), as well as hunted for food (only known from certain parts of Makira (C. Golden pers. comm.). Issues surrounding fady vary from region to region. Habitat destruction also threatens them throughout their range, with trees such as Intsia bijuga and Canarium madagascariensis – dietary staples for the species – being cut preferentially for the construction of boats, houses, and coffins (Iwano and Iwakawa 1988).

This species is listed on Appendix I of CITES.Daubentonia madagascariensis is reported to occur in numerous protected areas, including 13 national parks (Andohahela, Andringitra, Mananara-Nord, Mantadia, Marojejy, Masoala, Midongy du Sud, Montagne d' Ambre, Ranomafana, Sahamalaza-Iles Radama, Tsingy de Bemaraha, Tsingy de Namoroka, and Zahamena), seven strict nature reserves (Betampona, Tsaratanana, Makira, Farankaraina, Itampolo, Tsingy de Bemaraha, and Zahamena), and 13 special reserves (Ambatovaky, Analamazaotra, Analamerana, Anjanaharibe-Sud, Ankarana, Bora, Forêt d' Ambre, Kalambatritra, Manombo, Manongarivo, Marotandrano, Nosy Mangabe, and Pic d' Ivohibe). They are found as well in the forests of Daraina (part of the Loky-Manambato Protected Area), as well as in the Maroala and Anjiamanginana Classified Forests. Yet despite occuring in a great many protected areas, their presence is often based only on signs and infrequent sightings, so there is little understanding of population size and dynamics. There is an urgent need for a systematic census of this important flagship species throughout its range, with the ultimate objective of developing a conservation action plan for the species. As of 2010, there were approximately 50 aye-ayes in various zoological collections worldwide (ISIS 2009). There is a captive breeding program involving various institutions, and an EEP and a SSP. This species has not successfully bred in second generation in captivity.